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Remove one final invocation logger dep from autofocus

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This commit is contained in:
Julian Stirling 2025-12-17 09:49:00 +00:00
parent 09336c9cb5
commit e1dfceb0bd
3 changed files with 11 additions and 30 deletions
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14
src/openflexure_microscope_server/things/autofocus.py
View file

@ -484,28 +484,26 @@ class AutofocusThing(lt.Thing):
images_dir: str,
autofocus_dz: int,
save_resolution: tuple[int, int],
logger: lt.deps.InvocationLogger,
) -> StackParams:
"""Set up the parameters used for all stacks in a scan.
:param images_dir: the folder to save all images
:param autofocus_dz: the range to autofocus over if a stack fails
:param save_resolution: The resolution to save the captures to disk with
:param logger: A logger passed from the calling Thing
:returns: A StackParams object with the required parameters.
"""
# Coerce min_images_to_test parameter
min_images_to_test = self.stack_min_images_to_test
if min_images_to_test < MIN_TEST_IMAGE_COUNT:
logger.warning(
self.logger.warning(
f"Cannot test only {min_images_to_test} image(s) as this will fail. "
"Setting min images to test to lowest possible value of"
f"{MIN_TEST_IMAGE_COUNT}."
)
min_images_to_test = MIN_TEST_IMAGE_COUNT
elif min_images_to_test > MAX_TEST_IMAGE_COUNT:
logger.warning(
self.logger.warning(
f"Testing {min_images_to_test} images will cause defocus. "
"Setting min images to test to highest possible value of "
f"{MAX_TEST_IMAGE_COUNT}."
@ -513,7 +511,7 @@ class AutofocusThing(lt.Thing):
min_images_to_test = MAX_TEST_IMAGE_COUNT
elif min_images_to_test % 2 == 0:
min_images_to_test += 1
logger.warning(
self.logger.warning(
"Minimum number of images to test should be odd, setting to "
f"{min_images_to_test}."
)
@ -524,19 +522,19 @@ class AutofocusThing(lt.Thing):
# min_images_to_save
images_to_save = self.stack_images_to_save
if images_to_save <= 0:
logger.warning(
self.logger.warning(
"At least 1 images must be saved. Setting images to save to 1."
)
images_to_save = 1
elif images_to_save > min_images_to_test:
logger.warning(
self.logger.warning(
f"Cannot save {images_to_save} images as this above the minimum "
f"number to test. Setting images to save to {MAX_TEST_IMAGE_COUNT}."
)
images_to_save = min_images_to_test
elif images_to_save % 2 == 0:
images_to_save += 1
logger.warning(
self.logger.warning(
f"Images to save should be odd, setting to {images_to_save}."
)
# Set the Thing property to the coerced value

1
src/openflexure_microscope_server/things/smart_scan.py
View file

@ -378,7 +378,6 @@ class SmartScanThing(lt.Thing):
images_dir=self._ongoing_scan.images_dir,
autofocus_dz=self.autofocus_dz,
save_resolution=self._scan_data.save_resolution,
logger=self._scan_logger,
)
self._preview_stitcher = stitching.PreviewStitcher(
self._ongoing_scan.images_dir,

26
tests/test_stack.py
View file

@ -26,7 +26,6 @@ from openflexure_microscope_server.things.autofocus import (
_get_peak_turning_point,
)
LOGGER = logging.getLogger("mock-invocation_logger")
RANDOM_GENERATOR = np.random.default_rng()
@ -274,10 +273,7 @@ def test_create_stack(autofocus_thing, caplog):
initial_images_to_save = autofocus_thing.stack_images_to_save
with caplog.at_level(logging.INFO):
stack_params = autofocus_thing.create_stack_params(
autofocus_dz=2000,
images_dir="/this/is/fake",
save_resolution=(1640, 1232),
logger=LOGGER,
autofocus_dz=2000, images_dir="/this/is/fake", save_resolution=(1640, 1232)
)
assert len(caplog.records) == 0
@ -304,10 +300,7 @@ def test_coercing_stack_test_ims(
with caplog.at_level(logging.WARNING):
stack_params = autofocus_thing.create_stack_params(
autofocus_dz=2000,
images_dir="/this/is/fake",
save_resolution=(1640, 1232),
logger=LOGGER,
autofocus_dz=2000, images_dir="/this/is/fake", save_resolution=(1640, 1232)
)
assert len(caplog.records) == 1
@ -335,10 +328,7 @@ def test_coercing_stack_save_ims(
with caplog.at_level(logging.WARNING):
stack_params = autofocus_thing.create_stack_params(
autofocus_dz=2000,
images_dir="/this/is/fake",
save_resolution=(1640, 1232),
logger=LOGGER,
autofocus_dz=2000, images_dir="/this/is/fake", save_resolution=(1640, 1232)
)
assert len(caplog.records) == 1
@ -353,10 +343,7 @@ def test_coercing_stack_save_ims(
def test_run_smart_stack(pass_on, autofocus_thing, mocker):
"""Test Running smart stack with the stack passing on different attempts."""
stack_params = autofocus_thing.create_stack_params(
autofocus_dz=2000,
images_dir="/this/is/fake",
save_resolution=(1640, 1232),
logger=LOGGER,
autofocus_dz=2000, images_dir="/this/is/fake", save_resolution=(1640, 1232)
)
assert stack_params.max_attempts == 3
@ -417,10 +404,7 @@ def setup_and_run_z_stack(check_returns, check_turning_points, autofocus_thing,
results). If it a tuple (or anything else), it is set as a return value.
"""
stack_params = autofocus_thing.create_stack_params(
autofocus_dz=2000,
images_dir="/this/is/fake",
save_resolution=(1640, 1232),
logger=LOGGER,
autofocus_dz=2000, images_dir="/this/is/fake", save_resolution=(1640, 1232)
)
stack_params.settling_time = 0 # Don't settle or tests take forever.